I want to hook them up to atlas control boxes will it work if properly wired.
Yes
since the Bachmann switch wires are not colour coded, you will want to determine which is the common. this wire would go to the center of the 3 screw terminals on the top of the atlas control box. if using an ohm meter to test, the common wire should be the only one to get a continuity reading (low ohms) with the other two wires.
On every EZ-switch I've changed to use with push buttons, DS64 fixed decoders, or Atlas control boxes, the center wire was 'common'. Just flip the outside wires on the Atlas control box if the routes are reveresed from the way you want them.
Len